If Jonathan Survived City of Heavenly Fire
by Alicefreak101
Summary: DO NOT READ IF YOU HAVE NOT READ CITY OF HEAVENLY FIRE. THERE ARE SPOILERS SO DO NOT READ IF YOU HAVEN'T READ COHF. Summary inside. Rated T just to be safe. Some characters will be OOC.
1. Summary

If Jonathan Survived City of Heavenly Fire.

Summary: What would have happened if Jonathan survived City of Heavenly Fire? What if things were a whole lot different if he didn't die? Will the Clave trust him after what he has done to the Shadow World? Find out in If Jonathan Survived City of Heavenly Fire.


	2. Chapter 1

If Jonathan Survived City of Heavenly Fire

**A/N…Okay this is a story my friend Renesmee4eva and I came up with. She is my co-author for this story, so there will be days that I won't post as she lives in Australia and I live in the USA. The reason there will be no posts on some days are because we either have writers block or we are just very busy. So without further ado, we present you the first chapter of, If Jonathan Survived City of Heavenly Fire.**

**Also all quotes belong to Cassandra Clare.**

Chapter One

It wasn't till after Jonathan was stabbed with the sword. It was like his world was spinning around him as if he was on a merry go round. He could hear the blade clatter to the ground and see his mom and sister run towards him.

"Mom." Jonathan said weakly.

"Jonathan." Jocelyn said with a sigh knowing that this was the son she really wanted. The son with green eyes.

"I'm so sorry. I'm so sorry for everything." Jonathan said.

"It's alright." Clary said as she too kneeled down next to her brother.

Tears rimmed the three Morgenstern's eyes. Tears of pain and tears of sadness.

Darkness was starting to take over Jonathan. He was going in and out of consciousness.

"Jonathan please stay awake. We can still possibly save you." Jocelyn said.

"Mom, you can't. You should know what heavenly fire does to those who are evil. It kills them. I'm dying." Jonathan said.

"You can't die. I'm finally getting to see the real you. My real brother." Clary said as crystals fell from her face and landed on Jonathan.

"I know I wish I got to be with you more, but this is how it's supposed to be." Jonathan said as he continued to go in and out of consciousness.

Jocelyn and Clary just looked down at Jonathan as he closed his eyes.

"Magnus please you have to save him." Jocelyn cried.

"I can't. Heavenly fire destroys the evil inside them, but it also kills them if they were evil. He's gone." Magnus said.

"Please Magnus, please try." Clary cried as tears slipped down her cheek.

Both Clary and Jocelyn looked at Magnus with pleading eyes. Clary wanted to have her brother back, and Jocelyn wanted to have her son back, her real son.

"Please." Jocelyn cried as she continued to cradle Jonathan's head.

Magnus was hesitant at first, but then gave in.

"Alright, I will see what I can do." Magnus said.

Magnus started to use his powers and focused on Jonathan. Everyone that was in the room just looked as blue sparks flew from Magnus' finger tips and into Jonathan. A few minutes passed and just when he was about to give up, Jonathan started to breathe again. Magnus had done it. He had brought Jonathan back.

"I did it. He's alive, but it will take some time for him to recover. I don't know when he will wake up." Magnus said.

"Thank you." Jocelyn whispered as tears of joy slipped down her cheek.

Clary just hugged Magnus.

"Thank you Magnus." Clary cried with joy.

"We need to get out of here." Jace said.

"Right. However now that our only way out is closed we have to find another way out." Clary said.

"And how are we going to do that?" Isabelle asked.

"I have summon someone." Magnus said.

"Who?" Alec asked.

"My father." Magnus said as he started to concentrate on summoning his father. "My father, who are in Hell, unhallowed be thy name. Thy kingdom come, thy will be done, in Edom as it is in hell. Forgive not my sins, for in that fire of fires there shall be neither loving kindness, nor compassion, nor redemption. My father, who makes war in high places and low, come to me now; I call you as your son, and incur upon myself the responsibility of your summoning."

"By the Angel…" Alec started.

"No," said a voice just beyond their group. "Definitely not by your Angel."

"Father." Magnus said.

"My son why have you called upon me." Asmodeus said.

"Who are you?" Alec asked.

"I am Asmodeus." He said. "One of the Nine Princes of Hell. You may know my name."

"Can you send us back to Idris?" Magnus asked cutting back to business.

"Would you like a demonstration?" Asmodeus asked.

Asmodeus flicked his fingers and there was a shimmer of air as Luke, Jocelyn and an unconscious Jonathan , and the three of them were gone.

"Mom!" Clary shouted.

"I sent them back your world. Now you know." Asmodeus said as he examined his nails.

"How dare you." Clary said with rage.

"It's what you wanted. I sent them back, but to send the rest of you back; well it will cost you." Asmodeus said with a wicked smile.

"I know what you want." Magnus said in a strained voice. "And you can have it. But you must swear on the Morning Star to send all my friends back to Idris, all of them, and never to bother them again. They will owe you nothing."

"Magnus stop, what do you mean, what he wants? Why are you talking like you're not coming back to Idris with us?" Alec asked.

"There is a time," said Asmodeus, "when we must all return to live in the houses of our fathers. Now is Magnus's time."

"Magnus you can't do this." Alec said.

"Alec I must. It's the only way to send you back." Magnus said in a strained voice.

"There has to be another way." Jace said.

"There isn't," said Asmodeus, "I will simply take his immortality away and he will die."

"No! You can't do this Magnus, please." Alec pleaded as a crystal fell from his face.

"I'm sorry Alec, but I must. It's the only way to save you all. I love you so much." Magnus said as he kissed Alec on the lips. "Don't ever forget me."

"I won't." Alec said as he stepped back and stood by Jace and just leaned on him.

"All right." Magnus said. "All right, take me. I give you my life. I am…"

Simon, who had been silent till that moment; Simon, who Clary had almost forgotten was there stepped forward. "I am willing."

"Simon no!" Isabelle shouted, but Simon went on.

"I also have immortal life," he said. "Magnus isn't the only one. Take mine; take my immortality." Simon said bravely.

"Simon what are you doing?" Clary asked.

"I'm saving Magnus' life." Simon said.

"Simon." Isabelle said.

Simon just ignored Isabelle.

"I'm only seventeen. I won't die, I can live my life. Just do what you have to do and send my friends back." Simon said.

"Deal, however in order for your immortality to be taken, I must also take your memories." Asmodeus said as he looked at Simon with his cat eyes.

"Azazel took a memory from each of us, as payment for a favor," Alec said. "What is it with you demon and memories?"

"Human memories, freely given, are like food to us," said Asmodeus. "Demons live on the cries and agony of the damned in torment."

"Simon please don't do this. What am I supposed to do without my best friend?" Clary asked as tears started to flow down her face.

"He won't remember any of you." Asmodeus said.

"Let him go. He's ours, not yours." Jace said drawing his sword.

"Jace, don't. It's the only way. I am willing to sacrifice, my immortality and my memories to save you guys. It must be done." Simon said with a sigh.

Clary and Isabelle just cried as Asmodeus started to take away Simon's immortality and memories.

"No!" Clary shouted, as she tried to get to Simon, but only to be pulled back by Jace and Alec. "No let me go!" Clary shouted as she was dragged through the gateway. "Simon!" Clary shouted.

"Clary it's alright. It's going to be alright." Jace said.

"No it's not. He won't remember any of us." Clary cried as she tried to get away from Jace and Alec and go back through the gateway before it was closed.

"Oh no you don't." Alec said.

Clary just struggled in Jace and Alec's grip.

"Magnus." Alec called as he continued to hold onto Clary.

Magnus saw that Jace and Alec were struggling to keep Clary calm. The gateway had closed already, but Clary still hadn't calmed down.

"She won't calm down." Jace said.

"Let me go. I have to get Simon back." Clary said as she continued to struggle in Jace and Alec's arms.

Magnus just sighed and he soon used his powers to knock Clary out. Clary soon stopped struggling and just fell unconscious in Jace and Alec's arms.

Jocelyn and Luke then ran over to the others.

"What's going on? Where's Simon?" Jocelyn asked.

"In order for us to come back here, Asmodeus took away Simon's memories and immortality. He will no longer remember us." Isabelle said speaking for the first time since being in Edom.

"He saved my life. Asmodeus was going to take my immortality away and I would die there, but Simon took my place and now he is off living a mundane life." Magnus said.

Jocelyn just looked saddened and Luke just comforted her.

"I had knock Clary out as she was a little out of control." Magnus said. "How is Jonathan?"

"He's recovering. At first the Clave didn't want to believe that he was alive and no longer evil, but we managed to convince them and right now he is in the infirmary, resting." Luke said.

"Where are you staying at?" Jace asked.

"We're staying at Amatis' house." Jocelyn said.

"All right." Jace said getting up and taking Clary in his arms as Alec passed Clary to him.

With that Jace carried Clary to the house and after he laid her down in the bed that she once slept in, he left the house after saying night to Luke and Jocelyn and went back to the Penhallow's household with Alec who had followed him.

"Simon did a brave thing. If it wasn't for him then Magnus wouldn't be here right now." Alec said.

"That is true. I may have not gotten along with him, but he was brave enough to save us, to save Magnus." Jace said as he and his Parabatai walked into the house.

"If he ever does remember us, remind me to thank him for being brave." Alec said.

"I will if I remember to." Jace said.

The two best friends just laughed. Jace went to his room and Alec went to his room with Magnus.

**A/N…Okay so this is my new story. I hoped you all liked it. Now you may have noticed that I took quotes from the book. I'm not trying to plagiarize. If I were then I would not be giving credit to Cassandra Clare. This may be the only time I will use quotes, but then again if I used the quotes again, then I will give credit to Cassie. I mentioned above that all quotes belong to Cassie and, so without further ado I mention it again, the book City of Heavenly Fire belongs to Cassandra Clare. The quotes belong to Cassandra Clare. I own nothing, except the books as I love to read the books. I don't own her characters even though I want to own them, but I can't. **

**Please leave a review and no flames. This if the first time I am writing in third person and it was hard for me to write.**

**Chapter two will be up soon.**

**Bye.**


	3. What Should Happen in IJSCoHF

What should happen in If Jonathan Survived City of Heavenly Fire?

I know you thought this was an update, but sadly it's not. Don't worry, chapter two is being written right now. I just need some help on what should happen in the story. Just remember this isn't just going to be mainly focused on Jonathan, this is a continuation of City of Heavenly Fire, but of course with Jonathan in it since he survived. I am trying to become a professional writer and it is hard for me to write in third person as it is my first time doing it. Just let me know what should happen in the story. This is a list you can look at and just let me know by reviewing or sending me a Private Message. Thank you.

Should Maia forgive Jonathan for killing Jordan Kyle?

If Maia does forgive Jonathan should he ask her out as he starts to have feelings for Maia?

Should Magnus propose to Alec and there is a wedding?

Or should Jace propose to Clary and there is a wedding?

Both 3 and 4 should happen?

What should be Simons shadowhunter last name be once he is back in the story again and he remembers or well starts to remember things again?

When Simon does start to remember should he ask Isabelle out on a date?

How long do you want this story to be?


	4. Chapter 2

**A/N…Okay here is the second chapter to If Jonathan Survived City of Heavenly Fire. I am so happy to be getting reviews on my story. It's hard to write in third person, but at least I know what I am doing. So here is the next chapter. Also if I do use quotes from the book then I will of course give credit to Cassandra Clare. Now on with the chapter.**

Chapter Two

Clary awoke to the sun shining down on her face. She wasn't sure how she ended up in the bed that she slept in the last time she was in Idris. Then it hit her. Last night was a little a hazy after she lost her best friend. Simon. Simon who had sacrificed his immortality, and memories of the Shadow World. Just to save his friends. To save Magnus from dying, and never seeing Alec again. He did that to keep Alec and Magnus together. He may never remember Clary again. Especially Isabelle.

Clary hated Asmodeus for what he did. Why couldn't he just let them leave for free? Oh that's right, because demons always want something in return.

Clary was just getting out of bed when a knock came from the door.

"Come in." Clary called out.

Jace walked into the room. As usual he was gorgeous. His blonde hair shun in the sun light that shone through the window. And his gold eyes just sparkled.

"Morning, did you sleep well?" Jace asked as he walked over to Clary.

"Well after Magnus knocked me out, you could say that." Clary said.

Jace just chuckled.

"It's not funny Jace. I would have calmed down…eventually." Clary said.

"Eventually?" Clary you were in hysterics. We tried to get you to calm down, but we couldn't. We had no choice." Jace said coming towards Clary.

Clary just sighed and then looked at Jace.

"I'm going to go see Jonathan, do you want to come with me?" Clary asked. "Or are you going to go hang with Alec, Isabelle and Magnus?"

"I think I will go with you," said Jace. "Alec and Magnus are spending the day together. Isabelle is here, but I wanted to come up here alone to see you."

"Ah okay," said Clary. "Well then let me get dressed and I'll meet you and Isabelle downstairs."

"Alright, don't take too long or Isabelle will come up here with her whip and drag you down the stairs." Jace said with a laugh.

"Hey don't threaten me Jace Herondale!" Said Clary, "Or I'll make ducks chase after you!" Clary threatened.

"No!" Screamed Jace. "Not the ducks, anything but ducks!"

Clary just started laughing as she walked into the bathroom.

"Aw is Jace scared of ducks?" Isabelle asked.

"Shut up Isabelle." Jace said glaring at his sister.

Isabelle just laughed.

A few minutes passed and Clary came down the stairs dressed in a long sleeved black shirt and black pants with black boots on.

"Ready?" Clary asked grabbing her stele off the counter.

"Yeah." Jace and Isabelle said together.

The three of them were then off to the infirmary to see how Jonathan was.

"Morning." Jocelyn said to Clary and her friends as they walked in.

"Morning mom," said Clary. "How is he?"

"He's fine. We're hoping that he'll wake in the next few hours." Luke said.

"Well I'm glad that Sebastian is gone from him, and he is himself." Clary said sitting down next to her brother.

"I remember when I wasn't myself when I was connected to him." Jace said pulling up a chair next to Clary.

"That was a scary time for me. Especially Alec and Isabelle," said Clary. "They were both worried about you."

Jace just looked at Clary and smiled, "Well I'm here now," said Jace.

Jonathan had been in darkness for far too long. He thought that he was dead and that he was in Hell. Then he heard his mother's voice as well as his sister's voice. He was supposed to be dead. The Heavenly fire was supposed to kill him. He wasn't supposed to be alive, but he was. Finally after being in the dark abyss for a long time, he opened up his eyes to see a white ceiling. He then figured he was in the infirmary.

"Jonathan?" Clary asked as she hovered over her brother's face.

His eyes focused on Clary and he just smiled.

"Clary." Jonathan said.

Clary just smiled and gently hugged her brother. "How do you feel?" Clary asked.

"I feel fine," said Jonathan. "Where is mom?"

"Oh she and Luke stepped out for a little while," said Clary. "They went to get something to eat."

"I'm so sorry for everything Clary," said Jonathan. "I should be dead, but now I am glad that I'm not." Jonathan said smiling.

"So am I," said Clary. "And you don't have to keep apologizing. I've already forgiven you, and so has mom." Clary said as Jonathan sat up.

"I know it's just that I feel really guilty." Jonathan said.

"Stop feeling guilty." Clary said. "Please?"

"Alright." Jonathan said.

"Do you want some water?" Clary asked.

"Yeah, thanks."

Clary handed Jonathan his cup of water just as Jocelyn and Luke walked in.

"I'm going to go find Jace." Clary said getting up. "I'll be back later."

"Alright." Jonathan said.

"Magnus for the hundredth time do not put glitter on my clothes!" Alec exclaimed coming out of the bathroom that was connected to the bedroom that he and Magnus shared.

"I'm sorry my darling, but I just couldn't resist." Magnus said with a huge smile on his face.

"You think this is funny!" Alec shouted.

"Yes," said Magnus. "I think it is funny. You're so cute when you're mad." Magnus said coming up to Alec and then kissing him till he finally calmed down.

Alec just sighed.

"Just stop putting glitter on my clothes or next time you'll wake up to find all of your glitter washing away in the river." Alec said as he threatened his boyfriend.

"Okay that's just mean." Magnus said trying not to smile, but failing in the process of trying to be mad at Alec.

Alec just laughed just as Magnus started to laugh again.

"Seeing you mad, just makes me love you even more." Magnus said as he pulled Alec closer to him.

"Yeah, well like I said next time you won't have glitter if you put glitter on my clothes again." Alec said smiling before kissing Magnus.

Suddenly Magnus and Alec were making out, and then five minutes into the make out session, Alec and Magnus were half naked when Jace walked in.

"Hey Alec, Magnus when…" Jace just trailed off as he saw Magnus on top of Alec.

"Oh my Angel!" Jace shouted. "I don't want to see this!" Jace shouted again as he covered his eyes.

"Then get out." Magnus said.

"Gladly," said Jace. "I'll come back later."

Alec and Magnus just started to laugh.

"Mom, Luke I'm sorry for the pain that I have caused on everyone." Jonathan said.

"Jonathan, that was the past," said Jocelyn. "Just focus on the present and future."

"Alright," said Jonathan. "I really am sorry for stabbing you." Jonathan said to Luke.

"I forgive you Jonathan." Luke said smiling.

"When am I allowed to leave, because I'm ready to go home? I'm ready to go to my real home which I am guessing is in New York?" Jonathan asked.

"You should be able to go home soon. We're all going to leave together through a portal possibly within the next few days." Jocelyn said.

"I really do love you guys." Jonathan said.

"We love you too." Luke said.

Isabelle had just gotten back from taking a walk. As far as she knew Jace and Clary were still at the infirmary. She was still upset about the fact that she lost Simon. It was like losing Max again, but this time it was Simon. Yes, he's not dead, but she just misses him.

Isabelle was just thinking when there was knock on her door.

"Isabelle, can I come in?" Clary asked from behind the door.

"Sure." Isabelle said opening up the door for Clary.

"I was wondering where you ran off to," said Clary. "Have you seen Jace?"

"I thought he was with you." Isabelle said.

"No he left the infirmary hours ago, I just thought…" Clary was cut off when she and Isabelle heard a scream from the other side of the house.

It was Jace.

"What the hell was that about?" Clary asked.

Isabelle just shrugged.

"Maybe he ran into Magnus and he conjured up a duck." Isabelle said.

"Maybe so." Clary said.

Jace then came down the hall as the hall went around the house on the second story.

"Why did you scream like a girl?" Clary asked.

"I didn't scream like a girl." Jace said trying to act cool.

"Yes you did," said Clary. "Why did you scream?" Clary asked.

"I don't want to talk about it." Jace said.

"What, you walked in on Alec and Magnus?" Isabelle asked.

Jace just looked away.

"You did walk in on them!" Isabelle exclaimed before bursting out in laughter.

Clary just started to laugh.

"Aw is Jace embarrassed?" Clary asked in a little girl voice.

Jace just gave her a look and then smiled.

"Well, next time they need to lock the door." Jace said.

"I am never letting you live that down Jace." Isabelle said.

"Isabelle shut up." Jace said.

Clary just laughed again.

"You think this is funny?" Jace asked.

"Yes, I do think this is funny." Clary said as she continued to laugh.

"You won't be laughing after I throw you in the river." Jace said as he picked her up and threw her over his shoulder.

"Jace put me down!" Clary shouted as she pounded her fists against Jace's back.

Jace just laughed and continued to go down stairs.

"Jace, I'm serious! Put me down. It's the middle of winter and I don't want to get sick!" Clary shouted.

Magnus and Alec came out of their room and saw what was going on.

"Jace put Clary down unless you want to deal with her mother!" Magnus shouted from upstairs.

Jace just put Clary down.

"It wasn't like I was going to actually throw her into the river!" Jace shouted looking up only to see that Magnus was still half naked. Alec was also still half naked.

Clary just walked away from Jace and went back upstairs to Isabelle's room.

"Hey you guys want to come and tag along with me. I'm going back to the infirmary to see Jonathan again?" Clary asked looking at Magnus and Alec for the first time.

"Sure why not." Alec said.

"I'm in." Magnus said as he and Alec went back into their room and got dressed.

"You coming to Iz?" Jace asked coming back up the stairs.

"No, I think I'm going to stay here and just hang out in my room." Isabelle said.

"Izzy come on please. It's time we moved on. I mean yes I miss him, but we need to move on. Come on come with us." Clary said begging her friend.

"Fine, just give me five minutes." Isabelle said.

Clary just smiled and went to stand by Jace who was leaning against the wall.

"I swear Jace Herondale, next time you threaten to throw me into a river; you will find thousands of ducks in your room." Clary said threatening her boyfriend.

"No, anything but the ducks!" Jace shouted.

Clary just laughed as Magnus and Alec came out of the room.

"What's he shouting about this time?" Alec asked.

"I told him that next time he threatens to throw me into a river, he will find thousands of ducks in his room." Clary said still laughing.

"If I were you, I'd still put the ducks in his room." Magnus said.

"I agree with Magnus." Isabelle said coming out of her room.

"I think I might just do that." Clary said as the four friends laughed at Jace who was still running around shouting about killing ducks.

"Come on Jace, let's go you moron." Isabelle said dragging Jace by the collar of his shirt.

"I can walk thank you very much." Jace said.

Magnus just snapped his fingers and a duck appeared in front of Jace. Jace just screamed like a girl and hid behind Clary who was just laughing. Everyone except for Jace was now laughing.

"Sorry couldn't resist." Magnus said making the duck disappear.

"You're cruel Magnus Bane." Jace said.

"I know." Magnus said as he locked hands with Alec.

With that the five friends walked to the infirmary to see Jonathan.

**A/N…Alright that is it for chapter two. I hope you liked it. I had to put humor in the chapter. I mean what kind of story doesn't have humor in.**

**Please review and no flames.**

**Chapter three will be up soon.**

**Bye.**


	5. Authors Note for IJSCoHF

**Authors Note…**

**I know you guys were expecting this to be a chapter, but right now I am having major writers block and I just can't think of anything right now. I am about to start school next month and not only that, but I have a job and so I don't know when I am going to be posting the third chapter. I have already started writing it, but I just can't think of anything else to write. Hopefully I will think of what to write over the holiday break. On my other story No Ordinary Universe; I have no idea what to write next. I have to get in touch with my beta reader. So yeah, I wish that I could write more, but I really hate writers block. If you guys could help me then that will be amazing. I am going to put what I have of chapter three so far in this authors note, and if you have any ideas just let me know my either private messaging me, or leaving a review. Thanks.**

**Here is what I have for chapter three.**

Chapter Three

It has been a week since everything happened. Jonathan was released from the infirmary and now everyone was heading home. As everyone was walking to the portal, Clary and Jocelyn were arguing about how Clary can't stay at the institute.

"Mom, I need to keep training and I would rather stay at the institute. I don't want to keep going back and forth every day. I mean I stay there during the week and then come home on the weekends." Clary protested.

"Clary how many times have I told you? No. I will not allow it. Now stop asking." Jocelyn said.

"You never let me do what I want!" Clary shouted.

"That's enough. End of discussion." Jocelyn said annoyingly.

"Come on Clary, don't worry about her. You'll be there to train with us every day, even if you can't stay with us." Isabelle said.

"I know, but still. It's not like Jace and I are going to sleep in the same bed." Clary said.

"Yeah, but still you also have to be there for your brother." Alec said coming up behind the two friends, making Clary jump and making Alec and Isabelle laugh.

"It's not funny guys." Clary said.

"Sure it is." Magnus said as she came up next to Alec, making Clary jump again.

"Will you stop that?" Clary asked as Isabelle, Alec and Magnus laughed.

"Sorry, but it's funny when you get scared." Isabelle said.

Clary just rolled her eyes.

They soon arrived at the guard and the portal was open and ready for those who were leaving Idris.

"I guess I will see you guys on Monday morning for training." Clary said.

"Yeah, I guess so." Alec said.

"Where's Jace?" Clary asked.

"He's talking to Jonathan." Isabelle said.

"Wow I thought that he hated him." Clary said.

"No," Alec said. "Ever since we got back, Jace would be in the infirmary and they started talking and well now they are getting along. So now he and Jonathan are friends."

"Wow, I never thought that Jace and my brother would ever get along after what has happened." Clary said.

"I know it surprised me to." Isabelle said.

**Please let me know if you have any ideas thanks.**


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